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## T

TEXT_WIDTH - Static variable in class org.metaqtl.graph.QtlLayer
  The default width of the Text attribute of the Qtl
theta - Variable in class org.metaqtl.MultiFitResult
  The parameter estimates.
TICK_CEX_HEIGHT - Static variable in class org.metaqtl.graph.QtlLayer
  The default cex parameter for the tick height of the Qtl
TICK_CEX_WIDTH - Static variable in class org.metaqtl.graph.QtlLayer
  The default cex parameter for the tick width of the Qtl
TINY_MAPPING_DISTANCE - Static variable in interface org.metaqtl.IMetaQtlConstants
  The minimal distance in morgan
TINY_MAPPING_VARIANCE - Static variable in interface org.metaqtl.IMetaQtlConstants
  the minimal variance in morgan
TINY_Z_PROBA - Static variable in class org.metaqtl.algo.EMAlgorithm
  The minimal value for Z proba in EM-clustering
to - Variable in class org.metaqtl.Qtl.QTLSupport
  The position from the first marker to the right border of the IC.
toChromosome(IBioLGroup, IBioCross, int, int) - Static method in class org.metaqtl.adapter.ChromosomeAdapter
  This method converts a linkage group into a chromosome of type `Chromosome` with the given cross design and the given mapping context.
toChromosomes(IBioGenome) - Static method in class org.metaqtl.adapter.ChromosomeAdapter
  This methods converts the given map into an array of `Chromosome` which represents the chromosomes of the input mpe.
toEntity(BioEntityBean, IBioEntity) - Static method in class org.thalia.bio.entity.adapter.BioEntityAdapter
toEntity(Object) - Method in class org.thalia.bio.entity.adapter.BioEntityCollectionAdapter
toEntity(Object) - Method in class org.thalia.bio.entity.adapter.GeneticMapBeanAdapter
toEntity(Object) - Method in class org.thalia.bio.entity.adapter.LGroupBeanAdapter
toEntity(Object) - Method in class org.thalia.bio.entity.adapter.LocusBeanAdapter
toEntity(Object) - Method in class org.thalia.bio.entity.adapter.OntologyBeanAdapter
toEntity(Object) - Method in class org.thalia.bio.entity.adapter.OntologyTermBeanAdapter
toEntity(Object) - Method in interface org.thalia.bio.IBioAdapter
  Convert the given bio entity object into another compliant object.
toIBioGenome(Chromosome[], int) - Static method in class org.metaqtl.adapter.ChromosomeAdapter
  This routine converts an array of chromosomes into a genetic map with as many chromosomes as the length of the array.
toIBioGenome(MetaMap) - Static method in class org.metaqtl.adapter.MetaMapAdapter
  This methos convert a `MetaMap` object into an object which is consistent with the `IBioGenome` interface.
toQTL(IBioLocus) - Static method in class org.metaqtl.adapter.QtlAdapter
  This method converts an object which class implements the `IBioLocus`interface into a `Qtl`.``
toString() - Method in class org.metaqtl.Chromosome
toString() - Method in class org.metaqtl.MultiFitResult
toString() - Method in class org.thalia.bio.entity.LGroup
totd - Variable in class org.metaqtl.Chromosome
  The total distance of the chromosome.
trait - Variable in class org.metaqtl.MetaQtlResult
  The name of the trait.
trait - Variable in class org.metaqtl.Qtl
  The QTL trait data.
traitNames - Variable in class org.metaqtl.MetaQtlModel
  The trait names per chromosome.
transformY(double) - Method in class org.metaqtl.graph.ChromAxe
  Do a affine transformation of the given position `d` which is assumed to be in [0,dmax] in order to have its representation in the chromosome axe.
tree - Variable in class org.metaqtl.MetaQtlResult
  The qtl tree
tree - Variable in class org.metaqtl.QtlPartition
  The Qtl tree.
Tree - Class in org.metaqtl
  This class defines a tree.
Tree() - Constructor for class org.metaqtl.Tree
Tree(TreeNode) - Constructor for class org.metaqtl.Tree
tree_method - Variable in class org.metaqtl.algo.QtlTreeAlgorithm
  This global variable defines the method used by the aglomerative hierarchical clustering.
TREE_NODE_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
TreeFactory - Class in org.metaqtl.factory
  A factory to deal with distance trees.
TreeFactory() - Constructor for class org.metaqtl.factory.TreeFactory
TreeNode - Class in org.metaqtl
  This class represents a node in a binary Tree obtained when applying usual hirarchical clustering methods.
TreeNode(int) - Constructor for class org.metaqtl.TreeNode
  Creates a new instance of `TreeNode` with the given indice `idx`.
TreeNode(int, TreeNode[]) - Constructor for class org.metaqtl.TreeNode
  Creates a new instance of `TreeNode` with the given indice `idx` and the children of the node.
TreeNode() - Constructor for class org.metaqtl.TreeNode
  Creates a new instance of `TreeNode` with default attribute values.
type - Variable in class org.metaqtl.Qtl.QTLCross
  The type of the cross.
type - Variable in class org.thalia.bio.entity.bean.LocusBean
type - Static variable in class org.thalia.bio.util.BioCrossTypes
TypesString - Static variable in interface org.thalia.bio.IBioLocus
typeToString(int) - Static method in class org.thalia.bio.util.BioLocusTypes

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